BMB Reports

Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
권호 표지
DOI QR코드

DOI QR Code

Genomic approaches for the understanding of aging in model organisms

  • Park, Sang-Kyu (Department of Medical Biotechnology, College of Medical Science, Soonchunhyang University)
  • Received : 2011.04.18
  • Published : 2011.05.31
Download PDF
⟨ Previous Next ⟩

Abstract

Aging is one of the most complicated biological processes in all species. A number of different model organisms from yeast to monkeys have been studied to understand the aging process. Until recently, many different age-related genes and age-regulating cellular pathways, such as insulin/IGF-1-like signal, mitochondrial dysfunction, Sir2 pathway, have been identified through classical genetic studies. Parallel to genetic approaches, genome-wide approaches have provided valuable insights for the understanding of molecular mechanisms occurring during aging. Gene expression profiling analysis can measure the transcriptional alteration of multiple genes in a genome simultaneously and is widely used to elucidate the mechanisms of complex biological pathways. Here, current global gene expression profiling studies on normal aging and age-related genetic/environmental interventions in widely-used model organisms are briefly reviewed.

Keywords

References

  1. Herman, D. (1956) Aging: a theory based on free radical and radiation chemistry. J. Gerontol. 11, 298-300. https://doi.org/10.1093/geronj/11.3.298
  2. Boffoli, D., Scacco, S. C., Vergari, R., Solarino, G., Santacroce, G. and Papa, S. (1994) Decline with age of the respiratory chain activity in human skeletal muscle. Biochim. Biophys. Acta. 1226, 73-82. https://doi.org/10.1016/0925-4439(94)90061-2
  3. Short, K. R., Bigelow, M. L., Kahl, J., Singh, R., Coenen- Schimke, J., Raghavakaimal, S. and Nair, K. S. (2005) Decline in skeletal muscle mitochondrial function with aging in humans. Proc. Natl. Acad. Sci. U.S.A. 102, 5618- 5623. https://doi.org/10.1073/pnas.0501559102
  4. Best, B. P. (2009) Nuclear DNA damage as a direct cause of aging. Rejuvenation Res. 12, 199-208. https://doi.org/10.1089/rej.2009.0847
  5. Shay, J. W. and Wright, W. E. (2005) Senescence and immortalization: role of telomeres and telomerase. Carcinogenesis 26, 867-874. https://doi.org/10.1093/carcin/bgh296
  6. Johnson, T. E. (1990) Increased life-span of age-1 mutants in Caenorhabditis elegans and lower Gompertz rate of aging. Science 249, 908-912. https://doi.org/10.1126/science.2392681
  7. Kenyon, C., Chang, J., Gensch, E., Rudner, A. and Tabtiang, R. (1993) A C. elegans mutant that lives twice as long as wild type. Nature 366, 461-464. https://doi.org/10.1038/366461a0
  8. Clancy, D. J., Gems, D., Harshman, L. G., Oldham, S., Stocker, H., Hafen, E., Leevers, S. J. and Partridge, L. (2001) Extension of life-span by loss of CHICO, a Drosophila insulin receptor substrate protein. Science 292, 104-106. https://doi.org/10.1126/science.1057991
  9. Tatar, M., Kopelman, A., Epstein, D., Tu, M. P., Yin, C. M. and Garofalo, R. S. (2001) A mutant Drosophila insulin receptor homolog that extends life-span and impairs neuroendocrine function. Science 292, 107-110. https://doi.org/10.1126/science.1057987
  10. Brown-Borg, H. M., Borg, K. E., Meliska, C. J. and Bartke, A. (1996) Dwarf mice and the ageing process. Nature 384, 33.
  11. Lund, J., Tedesco, P., Duke, K., Wang, J., Kim, S. K. and Johnson, T. E. (2002) Transcriptional profile of aging in C. elegans. Curr. Biol. 12, 1566-1573. https://doi.org/10.1016/S0960-9822(02)01146-6
  12. Park, S. K. and Prolla, T. A. (2005) Gene expression profiling studies of aging in cardiac and skeletal muscles. Cardiovasc. Res. 66, 205-212. https://doi.org/10.1016/j.cardiores.2005.01.005
  13. Park, S. K. and Prolla, T. A. (2005) Lessons learned from gene expression profile studies of aging and caloric restriction. Ageing Res. Rev. 4, 55-65. https://doi.org/10.1016/j.arr.2004.09.003
  14. Pletcher, S. D., Macdonald, S. J., Marguerie, R., Certa, U., Stearns, S. C., Goldstein, D. B. and Partridge, L. (2002) Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster. Curr. Biol. 12, 712- 723. https://doi.org/10.1016/S0960-9822(02)00808-4
  15. Zou, S., Meadows, S., Sharp, L., Jan, L. Y. and Jan, Y. N. (2000) Genome-wide study of aging and oxidative stress response in Drosophila melanogaster. Proc. Natl. Acad. Sci. U.S.A. 97, 13726-13731. https://doi.org/10.1073/pnas.260496697
  16. Rea, S. L., Wu, D., Cypser, J. R., Vaupel, J. W. and Johnson, T. E. (2005) A stress-sensitive reporter predicts longevity in isogenic populations of Caenorhabditis elegans. Nat. Genet. 37, 894-898. https://doi.org/10.1038/ng1608
  17. Budovskaya, Y. V., Wu, K., Southworth, L. K., Jiang, M., Tedesco, P., Johnson, T. E. and Kim, S. K. (2008) An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegans. Cell 134, 291-303. https://doi.org/10.1016/j.cell.2008.05.044
  18. Golden, T. R. and Melov, S. (2004) Microarray analysis of gene expression with age in individual nematodes. Aging Cell 3, 111-124. https://doi.org/10.1111/j.1474-9728.2004.00095.x
  19. Johnson, T. E., Henderson, S., Murakami, S., de Castro, E., de Castro, S. H., Cypser, J., Rikke, B., Tedesco, P. and Link, C. (2002) Longevity genes in the nematode Caenorhabditis elegans also mediate increased resistance to stress and prevent disease. J. Inherit. Metab. Dis. 25, 197- 206. https://doi.org/10.1023/A:1015677828407
  20. McElwee, J., Bubb, K. and Thomas, J. H. (2003) Transcriptional outputs of the Caenorhabditis elegans forkhead protein DAF-16. Aging Cell 2, 111-121. https://doi.org/10.1046/j.1474-9728.2003.00043.x
  21. Murphy, C. T., McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H. and Kenyon, C. (2003) Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature 424, 277- 283. https://doi.org/10.1038/nature01789
  22. McElwee, J. J., Schuster, E., Blanc, E., Thomas, J. H. and Gems, D. (2004) Shared transcriptional signature in Caenorhabditis elegans Dauer larvae and long-lived daf-2 mutants implicates detoxification system in longevity assurance. J. Biol. Chem. 279, 44533-44543. https://doi.org/10.1074/jbc.M406207200
  23. Halaschek-Wiener, J., Khattra, J. S., McKay, S., Pouzyrev, A., Stott, J. M., Yang, G. S., Holt, R. A., Jones, S. J., Marra, M. A., Brooks-Wilson, A. R. and Riddle, D. L. (2005) Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res. 15, 603-615. https://doi.org/10.1101/gr.3274805
  24. Feng, J., Bussiere, F. and Hekimi, S. (2001) Mitochondrial electron transport is a key determinant of life span in Caenorhabditis elegans. Dev. Cell 1, 633-644. https://doi.org/10.1016/S1534-5807(01)00071-5
  25. Lakowski, B. and Hekimi, S. (1996) Determination of life-span in Caenorhabditis elegans by four clock genes. Science 272, 1010-1013. https://doi.org/10.1126/science.272.5264.1010
  26. Dillin, A., Hsu, A. L., Arantes-Oliveira, N., Lehrer-Graiwer, J., Hsin, H., Fraser, A. G., Kamath, R. S., Ahringer, J. and Kenyon, C. (2002) Rates of behavior and aging specified by mitochondrial function during development. Science 298, 2398-2401. https://doi.org/10.1126/science.1077780
  27. Durieux, J., Wolff, S. and Dillin, A. (2011) The cell-nonautonomous nature of electron transport chain-mediated longevity. Cell 144, 79-91. https://doi.org/10.1016/j.cell.2010.12.016
  28. Bishop, N. A. and Guarente, L. (2007) Two neurons mediate diet-restriction-induced longevity in C. elegans. Nature 447, 545-549. https://doi.org/10.1038/nature05904
  29. Chen, D., Thomas, E. L. and Kapahi, P. (2009) HIF-1 modulates dietary restriction-mediated lifespan extension via IRE-1 in Caenorhabditis elegans. PLoS Genet 5, e1000486. https://doi.org/10.1371/journal.pgen.1000486
  30. Greer, E. L., Dowlatshahi, D., Banko, M. R., Villen, J., Hoang, K., Blanchard, D., Gygi, S. P. and Brunet, A. (2007) An AMPK-FOXO pathway mediates longevity induced by a novel method of dietary restriction in C. elegans. Curr. Biol. 17, 1646-1656. https://doi.org/10.1016/j.cub.2007.08.047
  31. Panowski, S. H., Wolff, S., Aguilaniu, H., Durieux, J. and Dillin, A. (2007) PHA-4/Foxa mediates diet-restriction- induced longevity of C. elegans. Nature 447, 550-555. https://doi.org/10.1038/nature05837
  32. An, J. H. and Blackwell, T. K. (2003) SKN-1 links C. elegans mesendodermal specification to a conserved oxidative stress response. Genes Dev. 17, 1882-1893. https://doi.org/10.1101/gad.1107803
  33. An, J. H., Vranas, K., Lucke, M., Inoue, H., Hisamoto, N., Matsumoto, K. and Blackwell, T. K. (2005) Regulation of the Caenorhabditis elegans oxidative stress defense protein SKN-1 by glycogen synthase kinase-3. Proc. Natl. Acad. Sci. U.S.A. 102, 16275-16280. https://doi.org/10.1073/pnas.0508105102
  34. Park, S. K., Tedesco, P. M. and Johnson, T. E. (2009) Oxidative stress and longevity in Caenorhabditis elegans as mediated by SKN-1. Aging Cell 8, 258-269. https://doi.org/10.1111/j.1474-9726.2009.00473.x
  35. Park, S. K., Link, C. D. and Johnson, T. E. (2010) Life-span extension by dietary restriction is mediated by NLP-7 signaling and coelomocyte endocytosis in C. elegans. FASEB J. 24, 383-392. https://doi.org/10.1096/fj.09-142984
  36. Fares, H. and Greenwald, I. (2001) Genetic analysis of endocytosis in Caenorhabditis elegans: coelomocyte uptake defective mutants. Genetics 159, 133-145.
  37. Nathoo, A. N., Moeller, R. A., Westlund, B. A. and Hart, A. C. (2001) Identification of neuropeptide-like protein gene families in Caenorhabditiselegans and other species. Proc. Natl. Acad. Sci. U.S.A. 98, 14000-14005. https://doi.org/10.1073/pnas.241231298
  38. Lai, C. Q., Parnell, L. D., Lyman, R. F., Ordovas, J. M. and Mackay, T. F. (2007) Candidate genes affecting Drosophila life span identified by integrating microarray gene expression analysis and QTL mapping. Mech. Ageing Dev. 128, 237-249. https://doi.org/10.1016/j.mad.2006.12.003
  39. Kim, S. N., Rhee, J. H., Song, Y. H., Park, D. Y., Hwang, M., Lee, S. L., Kim, J. E., Gim, B. S., Yoon, J. H., Kim, Y. J. and Kim-Ha, J. (2005) Age-dependent changes of gene expression in the Drosophila head. Neurobiol. Aging 26, 1083-1091. https://doi.org/10.1016/j.neurobiolaging.2004.06.017
  40. Girardot, F., Lasbleiz, C., Monnier, V. and Tricoire, H. (2006) Specific age-related signatures in Drosophila body parts transcriptome. BMC Genomics 7, 69.
  41. Landis, G. N., Abdueva, D., Skvortsov, D., Yang, J., Rabin, B. E., Carrick, J., Tavare, S. and Tower, J. (2004) Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc. Natl. Acad. Sci. U.S.A. 101, 7663-7668. https://doi.org/10.1073/pnas.0307605101
  42. McCarroll, S. A., Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. S., Jan, Y. N., Kenyon, C., Bargmann, C. I. and Li, H. (2004) Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat. Genet. 36, 197-204. https://doi.org/10.1038/ng1291
  43. Lee, C. K., Klopp, R. G., Weindruch, R. and Prolla, T. A. (1999) Gene expression profile of aging and its retardation by caloric restriction. Science 285, 1390-1393. https://doi.org/10.1126/science.285.5432.1390
  44. Lee, C. K., Weindruch, R. and Prolla, T. A. (2000) Geneexpression profile of the ageing brain in mice. Nat. Genet 25, 294-297. https://doi.org/10.1038/77046
  45. Lee, C. K., Allison, D. B., Brand, J., Weindruch, R. and Prolla, T. A. (2002) Transcriptional profiles associated with aging and middle age-onset caloric restriction in mouse hearts. Proc. Natl. Acad. Sci. U.S.A. 99, 14988- 14993. https://doi.org/10.1073/pnas.232308999
  46. Lee, C. K., Pugh, T. D., Klopp, R. G., Edwards, J., Allison, D. B., Weindruch, R. and Prolla, T. A. (2004) The impact of alpha-lipoic acid, coenzyme Q10 and caloric restriction on life span and gene expression patterns in mice. Free Radic. Biol. Med. 36, 1043-1057. https://doi.org/10.1016/j.freeradbiomed.2004.01.015
  47. Park, S. K., Page, G. P., Kim, K., Allison, D. B., Meydani, M., Weindruch, R. and Prolla, T. A. (2008) alpha- and gamma-Tocopherol prevent age-related transcriptional alterations in the heart and brain of mice. J. Nutr. 138, 1010-1018. https://doi.org/10.1093/jn/138.6.1010
  48. Park, S. K., Kim, K., Page, G. P., Allison, D. B., Weindruch, R. and Prolla, T. A. (2009) Gene expression profiling of aging in multiple mouse strains: identification of aging biomarkers and impact of dietary antioxidants. Aging Cell 8, 484-495. https://doi.org/10.1111/j.1474-9726.2009.00496.x

Cited by

  1. Ageing as a Risk Factor for Disease vol.22, pp.17, 2012, https://doi.org/10.1016/j.cub.2012.07.024
  2. DEFOG: discrete enrichment of functionally organized genes vol.4, pp.7, 2012, https://doi.org/10.1039/c2ib00136e
  3. Conservation of pro-longevity genes among mammals vol.146-148, 2015, https://doi.org/10.1016/j.mad.2015.03.004
  4. The Frequency of 4 Common Gene Polymorphisms in Nonagenarians, Centenarians, and Average Life Span Individuals vol.65, pp.3, 2014, https://doi.org/10.1177/0003319712475075
  5. Bradykinin Inhibits Oxidative Stress-Induced Cardiomyocytes Senescence via Regulating Redox State vol.8, pp.10, 2013, https://doi.org/10.1371/journal.pone.0077034
  6. Possible Role of −374T/A Polymorphism of RAGE Gene in Longevity vol.14, pp.11, 2013, https://doi.org/10.3390/ijms141123203